KeyBase

Linking KeyBase to Symbiota taxon pages.

KeyBase (http://keybase.rbg.vic.gov.au/) has a useful set of tools for presenting dichotomous keys. Once a key is uploaded, it can be viewed in three different formats (see, for example, http://keybase.rbg.vic.gov.au/keys/show/6989, a key to grass tribes in North America north of America which is taken from FNA 24 (with permission of the copyright holder, Utah State University).

A few of the tribes and a few genera of Poeae have been linked to the appropriate taxon page in SEINet (http://intermontainbiota.org). They show up in a different color on the screen. Names that link to a lower level key (e.g., from the tribal key to a generic key) are followed by an arrow head; clicking on it will open the lower level key. 

Uploading a key

The keys have to be presented as a csv file with 3 columns and no headers:

  1. The first column contains the lead number, the second column the lead itself, and the third column the name of a taxon or the number of the lead to go to next.
  2. Lead numbers should be identical within a pair, i.e., 1 and 1, not 1a and 1b.
  3. The third column must contain either a name or a number; it cannot be left blank.

The order in which the leads are listed does not matter so long as the above requirements are met.

To upload a key, first register with the site, then click on projects (just above the banner), then scroll to the bottom of the page and click “Create new project”. From then on in, it is pretty straightforward. 

Filtering a key

KeyBase can filter the leads in a key so only the leads that lead to one of the filtered taxa are shown. For example, if one had a list of the grasses in a state of county of the US, these could be uploaded as a filter. To activate the filter, users would simply have to click the filter symbol at the top right of the key page and select the appropriate filter. The key will then display only leads that lead to one of the included taxa. This would be a great feature, for example, for generating state keys from the FNA keys. 

Linking to taxon page

To link taxon pages to the appropriate key in a project, one first needs to construct a 2 column csv file. The first column contains the name, the second the url of the taxon page. Again, do not have a header row.

Aira http://intermountainbiota.org/portal/taxa/index.php?taxon=17407
Beckmannia http://intermountainbiota.org/portal/taxa/index.php?taxon=4450

 

To upload these links, first ask Niels Klazenga (niels.klazenga@rbg.vic.gov.au) for permission to access the development version of KeyBase. Once in that version, there will be a heading “Items”. Click on it and upload your file. You can upload them all at once.

SUGGESTION:  

Clearly, automating the linking process would be highly desirable.  For enabling the keys to link to taxon pages, a user needs to able to select a list of taxon names from the taxonomic viewer (or submit a list to the Symbiota instance) and receive a csv download of those names with the relevant taxon page.

For embedding a link to the key for a next lower rank, there needs to be a way to generate the necessary text to embed at the end of the description on the taxon page. For example, on the description page for Calliandra in OpenHerbarium, the html version of the last statement is <p>Key to taxa of <a href=”http://keybase.rbg.vic.gov.au/dev/keys/show/8051″>Pakistan</a></p>. This takes one to the appropriate key in KeyBase.

Terminology Teacher

This is an idea I have only just begun to explore

Terminology is often a major obstacle for those entering a discipline. In systematic biology (and probably other fields) terminology can be thought of as strongly hierarchical, particularly with respect to structures. I am exploring the use of a KeyBase-Symbiota combination for learning botanical terminology. For example, the highest rank could have two members: Vegetative and Reproductive. Below Vegetative, Above-ground and Below-Ground …..  Yes, terms could simply be put in a book/pdf but my thought is that the combination of a dichotomous key and the similar structure of taxon pages would help students learn the terminology needed to make progress. If nothing else, it would be an alternative to different approaches. I envision having leaf scans and asking students to determine how to describe them. 

Desirable modifications in Symbiota:

  1. Constructing an alternative to the present nomenclatural hierarchical structure, one that has no restrictions on the number of words used at a given level and, ideally that, instead of using named taxonomic levels uses Level 1, Level 2, etc.
  2. Modifying the flash card quiz game so that students were asked to select multiple words that would apply to the structure presented.

So far, I cannot see the need for any modifications in KeyBase for this use so Niels. You can consider this an FYI item.